Cleaned up typos and tweaked one instruction to have it be run in the…

… terminal rather than the Jupyter notebook

GoogleCloud/submodule07_error_mitigation.ipynb

@@ -198,7 +198,9 @@
    "cell_type": "code",
    "execution_count": null,
    "id": "1f288b81-4a97-4755-aff0-118187882833",
-   "metadata": {},
+   "metadata": {
+    "scrolled": true
+   },
    "outputs": [],
    "source": [
     "# FLASHCARD\n",
@@ -270,21 +272,15 @@
     "\n",
     "In submodule 6 we needed to create two separate conda environments for assembly and annotation. I explained that this was due to a conflict in the dependencies of software used in each environment. \n",
     "\n",
-    "Let's try to install prokka in your assembly environment and see what error is thrown. Remember to set the kernel in the top left corner to `conda env:assembly`. "
+    "Let's try to install prokka in your assembly environment and see what error is thrown. Remember to activate your assembly environment in the terminal using `conda activate assembly`. This command will take about 10-15 minutes to run."
    ]
   },
   {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "22d02992-bb26-4b0c-adb5-8d258dd6fb98",
+   "cell_type": "markdown",
+   "id": "f40be959-a310-4cbf-b775-062645a814a5",
    "metadata": {},
-   "outputs": [],
    "source": [
-    "%%bash\n",
-    "\n",
-    "# add the prokka software to the assembly environment\n",
-    "# this command is going to take 10-15 minutes to run\n",
-    "conda install -c bioconda prokka=1.14.6"
+    "`conda install -c bioconda prokka=1.14.6`"
    ]
   },
   {
@@ -320,7 +316,31 @@
    ]
   }
  ],
- "metadata": {},
+ "metadata": {
+  "environment": {
+   "kernel": "conda-base-py",
+   "name": "workbench-notebooks.m128",
+   "type": "gcloud",
+   "uri": "us-docker.pkg.dev/deeplearning-platform-release/gcr.io/workbench-notebooks:m128"
+  },
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel) (Local)",
+   "language": "python",
+   "name": "conda-base-py"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.10.16"
+  }
+ },
  "nbformat": 4,
  "nbformat_minor": 5
 }